Longitudinal genomic analysis of Neisseria gonorrhoeae transmission dynamics in Australia

N. gonorrhoeae, which causes the sexually transmissible infection gonorrhoea, remains a significant public health threat globally, with challenges posed by increasing transmission and antimicrobial resistance (AMR). The COVID-19 pandemic introduced exceptional circumstances into communicable disease control, impacting the transmission of gonorrhoea and other infectious diseases. Through phylogenomic and phylodynamic analysis of 5881 N. gonorrhoeae genomes from Australia, we investigated N. gonorrhoeae transmission over five years, including a time period during the COVID-19 pandemic. Using a novel cgMLST-based genetic threshold, we demonstrate persistence of large N. gonorrhoeae genomic clusters over several years, with some persistent clusters associated with heterosexual transmission. We observed a decline in both N. gonorrhoeae transmission and genomic diversity during the COVID-19 pandemic, suggestive of an evolutionary bottleneck. The longitudinal, occult transmission of N. gonorrhoeae over many years further highlights the urgent need for improved diagnostic, treatment, and prevention strategies for gonorrhoea.


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Policy information about availability of computer code Data collection In Australia, all gonorrhoea cases are notified to public health authorities in each State or Territory.All N. gonorrhoeae isolated in Victoria from diagnostic laboratories were forwarded to the state Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL) for AMR surveillance purposes.Between 1 January 2017 to 31 December 2017 and 1 July 2019 to 30 June 2021 (inclusive), all forwarded isolates underwent antimicrobial susceptibility testing by agar dilution and WGS.Between 1st January 2018 and 30th June 2019 (inclusive) routine WGS was not conducted, and no isolates were sequenced.Information on gonorrhoea notifications in Victoria was obtained from the National Notifiable Diseases Surveillance System (NNDSS).

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